ORIGINAL RESEARCH article

Front. Plant Sci.

Sec. Plant Breeding

Volume 16 - 2025 | doi: 10.3389/fpls.2025.1632888

Assessing Genetic Redundancy and Diversity in Colombian Cacao Germplasm Banks using SNP fingerprinting

Provisionally accepted
Jaime A Osorio-GuarínJaime A Osorio-Guarín1Jhon A Berdugo-CelyJhon A Berdugo-Cely1Gina A Garzón-MartínezGina A Garzón-Martínez1Deisy Lisseth Toloza-MorenoDeisy Lisseth Toloza-Moreno1Paola Delgadillo-DuranPaola Delgadillo-Duran1Eliana Y Báez-DazaEliana Y Báez-Daza2Lyndel MeinhardtLyndel Meinhardt3Sunchung ParkSunchung Park3Dapeng ZhangDapeng Zhang3*Roxana YocktengRoxana Yockteng1*
  • 1Corporacion Colombiana de Investigación agropecuaria (AGROSAVIA), Mosquera, Colombia
  • 2Corporacion Colombiana de Investigación agropecuaria (AGROSAVIA), Rionegro (Santander), Colombia
  • 3USDA-ARS Beltsville Agricultural Research Center, Beltsville, United States

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Cacao germplasm is the cornerstone of sustainable cacao production, underpinning efforts to develop high-yielding, quality-rich, and climate-resilient varieties. This study aimed to evaluate the mislabeling, the genetic redundancy, and diversity of two cacao germplasm banks maintained at the Palmira and La Suiza research centers of the Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), from Colombia. We genotyped 4,653 cacao trees from these collections, and after applying quality control filters, a final set of 77 SNP markers was used for all subsequent analyses. Our results revealed that both collections exhibit a similar pattern of genetic diversity. However, a medium rate of mislabeling (12.4 %) and high genetic redundancy (53.1%) were detected, likely due to errors in collecting, introduction, pre-planting labeling, and the use of rootstocks. To optimize the evaluation conserved cacao germplasm, we defined core collections independently, which comprise 246 and 190 samples for Palmira and La Suiza, respectively. This research demonstrates the importance of maintaining a well-classified cacao collection with minimal genetic redundancy, thereby improving accuracy and reducing maintenance costs. This will not only enhance conservation efforts but also enrich the genetic diversity

Keywords: Breeding, Cacao, Duplicate, Germplasm banks, KASP, Mislabeling, molecular marker

Received: 21 May 2025; Accepted: 23 Jun 2025.

Copyright: © 2025 Osorio-Guarín, Berdugo-Cely, Garzón-Martínez, Toloza-Moreno, Delgadillo-Duran, Báez-Daza, Meinhardt, Park, Zhang and Yockteng. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Dapeng Zhang, USDA-ARS Beltsville Agricultural Research Center, Beltsville, United States
Roxana Yockteng, Corporacion Colombiana de Investigación agropecuaria (AGROSAVIA), Mosquera, Colombia

Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.

Supplementary Material